I'm certainly not angry. You don't need to worry about PCs using Threat to stun opponents unconscious as the GM is by default in charge of their expenditure. The combat sections of the CRBs spells out the steps by which a dice pool is evaluated. I think that addresses your two primary concerns.
My understanding was that the GM gets to spend Player Threat and NPC Advantage, while the Players spend PC Advantage and NPC threat. If it ain't it should be. Using threat to knock opponents out will only really work on minions (who cares?) softened-up rivals (again, who cares?) and Nemeses who have been spending strain like candy. Just be sure to describe it. The stormtroopers open fire on the PC's cover, and one of them takes a blaster bolt, collapsing. The bounty hunter grapples with the PC, only to discover that headbutting a Wookiee doesn't end well. The Inquisitor attacks with his lighsaber, hoping to finish the fight, only to be disarmed, kicked hard in the stomach, and is now on his knees at the mercy of the player.
The issue is that the GM has rule 0. Yes, you're right, it should "feel" that the GM spends NPC advantages and PC threat, and the players spend PC advantages and NPC threat. In actuality, however, the GM controls all of it. The task of a good GM is to hide that fact.
RPG rule books contain standardized guidelines of play. Things that, assuming all players familiarize themselves with, give a common language with which to engage in the story. They allow for certain levels of predictability.
However, it is the task of the GM to facilitate the story. Something that, while partly tied to the rules of the game, should in absolutely no way, be hindered by said rules. Say for example a GM -really- needs a villain NPC to escape a conflict, otherwise the entire rest of the campaign stops short, then the GM has every right to inform the players that some way they are trying to spend their PC advantage/NPC threat won't work (or rather, the GM should politely notify them that such an allocation of the points won't do them much good, and await a "better" use of the advantages/threat).
Edited by KommissarK